I would say the Confederate flag is controversial today for two major reasons. The Confederates were known for both rebelling against the Union and supporting slavery, which the Confederate flag can represent.
The Confederate flag represents the Confederacy, which were states that rebelled against the Union during the Civil War. The main reason why the Southern states wanted to secede from the Union was because of the issue of slavery. The South was in favor of slavery, while a lot of people in the North found it useless, immoral, or even wanted to abolish it completely. This was because the South relied on slavery to make their income, as they needed slaves to help on plantations. The North was focused on industrialization, so they had no need for slaves.
The Southern states, or the Confederates, then rebelled against the Union and a Civil War broke loose. Even after the Civil War ended and slavery was abolished, many former Confederates would go out of their way to harm African Americans and stop them from voting, even in extreme cases joining the Ku Klux Klan. This hate would not stop at just African Americans but then would spread to immigrants and women later on.
The Confederate flag is controversial because a lot of people believe that it stands for things the Confederates fought for or favored, like segregation, slavery, rebelling, etc. The Confederates fought for terrible things like slavery and tried to justify it, all while using the Confederate flag, that is why it is now controversial today.